Page 1 of 1

MASCOT Search

Posted: Mon Mar 04, 2013 12:36 pm
by Dania.Awad
Hello,
I am running a nanoflow LC followed by MSMS using MALDI TOF TOF. I am still optimizing my method using a BSA digest.
Luckily everything went well (so far), but I still need to identify the BSA by the mascot server search. I am not sure which options to choose in the mascot website. I would appreciate any help in guiding me through my next step.

Thank you

Posted: Thu Mar 07, 2013 2:31 am
by achimt
Dear Dania,

have a look at the following:
http://www.matrixscience.com/help.html
http://www.matrixscience.com/training_webcast.html

You might need your own licensed server to search your LCMSMS data. If you want to try a free search engine, there are several around, such as X!Tandem (http://www.thegpm.org), OMSSA (http://pubchem.ncbi.nlm.nih.gov/omssa/) or others.

Hope this helps,
Achim

Posted: Mon Mar 11, 2013 10:02 am
by aky
Choose trypsin, missed cleavage 1, Contaminants (or cRAP) as database (or swissprot) , Carbamidomethylation as fixed mod and Methioinine Oxidation as variable mod. Rest can be left default, though a tolerance of 0.2-0.5 Da should be fine for both precursor and fragments (neither too strict, nor too loose).